Objective: To detect the early preclinical alterations in cardiac autonomic control as well as altered cardiac function in systemic sclerosis (SSc) patients and their relevance to the clinical features of the disease using noninvasive methods. Methods: 30 SSc patients and 15 healthy controls matched for age and sex underwent clinical examination, serological analysis, and echocardiographic assessment including Doppler flow imaging to evaluate cardiac function, and 24-hour Holter monitoring analyzed for arrhythmia and heart rate variability (HRV) in the time and frequency domains. Results: The trans-mitral Doppler of early to atrial wave (E/A) ratio was reversed in five patients (16.6%) and the tricuspid E/A ratio was reversed in 10 patients (33.3%). Holter analysis for SSc patients revealed an increased prevalence of premature ventricular contractions (PVC) $ 10/h (P = 0.02), supra-ventricular tachycardias (SVTs) (P = 0.2), and total PVC count (P = 0.0000). Highly significant (P = 0.000) impairment in all HRV parameters was demonstrated in the SSc patients. Total skin thickness score (TSS), Raynaud's phenomenon and anti-scleroderma 70 (anti-SCL70) showed significant positive correlations with all arrhythmia parameters, while showing a significant negative correlation with the impaired ventricular diastolic function and various HRV parameters. No correlation was found between arrhythmia and HRV parameters and disease duration, disease type, or presence of anti-centromere antibodies. Conclusion: Low heart rate variability, increased TSS and the presence of anti-SCL70 are correlated with preclinical cardiac involvement in SSc patients and may predict the likelihood of malignant arrhythmia and sudden cardiac death. Therefore, noninvasive HRV evaluation before clinical cardiac involvement in these patients might be beneficial when added to the clinical and laboratory assessments in detecting high-risk patients, and may allow for implementation of preventive measures and initiation of appropriate therapy early in the course of the disease.